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UK e-Science Grid Infrastructure meets Biological Research Challenges Malcolm Atkinson Director of National e-Science Centre www.nesc.ac.uk 2 nd October.

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Presentation on theme: "UK e-Science Grid Infrastructure meets Biological Research Challenges Malcolm Atkinson Director of National e-Science Centre www.nesc.ac.uk 2 nd October."— Presentation transcript:

1 UK e-Science Grid Infrastructure meets Biological Research Challenges Malcolm Atkinson Director of National e-Science Centre 2 nd October 2002 The UK Biological Grid Data and Computation The Wellcome Trust Genome Campus Hinxton, Cambridgeshire

2 Overview UK e-Science Reminder of Investment and Infrastructure International e-Science Examples and Collaboration Data Access and Integration Lego Bricks for Scientific Application Developers A Computer Scientists View of Biology Diversity and Opportunity The Way Ahead

3 e-Science Fundamentally about Collaboration Sharing Ideas Thought processes and Stimuli Effort Resources Requires Communication Common understanding & Framework Mechanisms for sharing fairly Organisation and Infrastructure Scientists (Biologists) have done this for Centuries

4 e-Science (take 2) Fundamentally about Collaboration Sharing Ideas Thought processes and Stimuli Effort Resources Requires Communication Common understanding & Framework Mechanisms for sharing fairly Organisation and Infrastructure Text, digital media, structured, organised & curated data, computable models, visualisation, shared instruments, shared systems, shared administration, … Nationally & Internationally Distributed, … Routine, Daily, Automated, … That Requires very Significant Investment in Digital Systems and their Support

5 e-Science (take 3) Fundamentally about Collaboration Sharing Ideas Thought processes and Stimuli Effort Resources Requires Communication Common understanding & Framework Mechanisms for sharing fairly Organisation and Infrastructure Digital networks, digital work- places, digital instruments, … Metadata, ontologies, standards, shared curated data, shared codes, … Common platforms, shared software, shared training, … The Grid SHOULD make this much easier by providing a common, supported high-level of Software and Organisational infrastructure Authentication, Authorisation, Accounting, Provenance, Policies, … Shared Provision of Platform,

6 Grid Expectations Persistence Always there, Always Working, Always Supported Stability You can build on foundations that dont move Trustworthy & Predictable Honours commitments Digital policies, digital contracts, security, … Data integrity, longevity and accessibility Performance High-level & Extensible The capabilities you need are already there Ubiquitous Your collaborators use it

7 Grid Reality Persistence Always there, Always Working, Always Supported Stability You can build on foundations that dont move Trustworthy & Predictable Honours commitments Digital policies, digital contracts, security, … Data integrity, longevity and accessibility Performance High-level & Extensible The capabilities you need are already there Ubiquitous Your collaborators use it Political, Economic & Technical issues to Solve Early days but Open Grid Services link with Web Services + GGF standardisation Not yet but very substantial global effort to achieve this Good basis for extension Commitment to basic functionality WS + Community effort Global & Industrial Rallying Cry Must work with Web Services

8 Cambridge Newcastle Edinburgh Oxford Glasgow Manchester Cardiff Southampton London Belfast Daresbury Lab RAL Hinxton UK Grid Network National e- Science Centre always-on video walls Access Grid always-on video walls HPC(x)

9 National e-Science Centre Events Workshops Research Meetings International Meetings History of Events GGF5 HPDC11 Summer school > 50 workshops held > 1000 people in total Many return often Planned Events 25 workshops Conferences to 2005 Visitors 3 arrived 4 arranged International collaboration, visits & visitors China Argonne National Lab SDSC NCSA … Centre Projects Pilot Projects Regional Support Research Projects EPSRC, MRC, WT, SHEFC

10 A day in the life of NeSC

11 DOE X-ray grand challenge: ANL, USC/ISI, NIST, U.Chicago tomographic reconstruction real-time collection wide-area dissemination desktop & VR clients with shared controls Advanced Photon Source Online Access to Scientific Instruments archival storage From Steve Tuecke 12 Oct. 01

12 UCSF UIUC From Klaus Schulten, Center for Biomollecular Modeling and Bioinformatics, Urbana-Champaign

13 DataGrid Testbed Dubna Moscow RAL Lund Lisboa Santander Madrid Valencia Barcelona Paris Berlin Lyon Grenoble Marseille Brno Prague Torino Milano BO-CNAF PD-LNL Pisa Roma Catania ESRIN CERN HEP sites ESA sites IPSL Estec KNMI (>40) - Testbed Sites

14 A Simplified Grid Anatomy Grid Plumbing & Security Infrastructure SchedulingAccountingAuthorisation MonitoringDiagnosisLogging Scientific Application Data & Compute Resources Operations Team Application Developers Distributed Owners Scientific Users

15 A Biological Grid Anatomy Grid Plumbing & Security Infrastructure SchedulingAccountingAuthorisation MonitoringDiagnosisLogging Scientific Application Data & Compute Resources Distributed Biological Users Data Access Data Integration Structured Data

16 Database Growth PDB protein structures

17 Scientific Data Deluge of Data Exponential growth Doubling times Astronomy12 months Bio-Sequences9 months Functional Genomics6 months Bytes/dollar12 to 18 months Not How big it is but

18 Scientific Data Deluge of Data Exponential growth Doubling times Astronomy12 months Bio-Sequences9 months Functional Genomics6 months Bytes/dollar12 to 18 months Not How big it is but What you do with it Sharing Curation Metadata Automated movement, access & integration Computational Access

19 Scientific Data Deluge of Data Exponential growth Doubling times Astronomy12 months Bio-Sequences9 months Functional Genomics6 months Bytes/dollar12 to 18 months Not How big it is but How you Embrace & Manage Change The Database is a Knowledge chest The Database is a Communication Hub Autonomously Managed (Curated) change An Essential part of e-BioMedical Science

20 Wellcome Trust: Cardiovascular Functional Genomics Glasgow Edinburgh Leicester Oxford London Netherlands Shared data Public curated data

21 Data Access & Integration Central to e-Science Especially Earth Sciences, Ecology, Biology & Medicine Collaboration Shared Databases Curated Knowledge Accumulated Observations Accumulated Simulations Computation Data mining Input to models Calibration of models Presentation Publication of results Visualisation

22 GGF DAIS WG Chairs Norman Paton (Manchester Uni.) Leanne Guy (CERN) Dave Pearson (Oracle UK) Activity BoF GGF4 Toronto WG Meeting GGF5 Edinburgh Papers for GGF6 Workshops & Mail lists Goals Agree Standards for Database Access & Integration Freely available reference implementations OGSA-DAI one source & focus for discussions Norman Paton, Inderpal Narang, Leanne Guy, Susan Maliaka, Greg Ricardi, …

23 OGSA-DAI project Lego kit for Data Access & Integration Components for e-Science Applications Accelerated Application Development Multiple Data Models Distributed Data Access via Grid & Proxies Integration, Translation & Transformation Open Source Reference Implementation For DAIS-WG standard Trigger for Component Construction Start a community

24 Oxford Glasgow Cardiff Southampton London Belfast Daresbury Lab RAL OGSA-DAI Partners EPCC & NeSC Newcastle IBM USA IBM Hursley Oracle Manchester EPCC & NeSC IBM UK IBM USA Manchester e-SC Newcastle e-SC Oracle £3 million, 18 months, started February 2002 Cambridge Hinxton

25 Primary Components

26 Advanced Components

27 Composed Components

28 Distributed Query

29 OGSA-DAI Time Line Feb 02May 02Jul 02Sep 02Dec 02Feb 03May 03Sep 03 Ship Alpha Release for GT3 Integration RDB + GT2 / OGSA Prototypes Available XML + OGSA Prototype Available Design Documents & Demos for DAIS GGF5 XML + OGSA Prototypes for Early Adopters WS + GSI UK support ( > 100 downloads) Phase 2 Starts Phase 1 Starts Presentation & GGF7 GGF6 WG Papers & Prototypes Productisation, RAMPS & Extension

30 OGSA-DAI Summary On Schedule & Going Well Contributions via GGF5 & 6 Releases with GT3 Releases scheduled Status: Early Days Released prototypes Tested Architectural Design Using OGSA Working with Early Adopter Pilot Projects AstroGrid & MyGrid Influence OGSA-DAI direction Via DAIS-WG & Direct messages to us

31 Biomedical e-Scientists Is this one species? Understanding bird energy Understanding a river / ocean interaction Understanding a biochemical pathway Understanding a cell Understanding a Heart or Brain Understanding Rhododendra Understanding Evolution … No One-Size fits all solutions But sharable re-usable components

32 Opportunities Many, many … More than we can address Compute needs Data management needs Data integration needs … Must choose some pioneers To meet a range of common requirements To provoke rich & high-level platform To generate re-usable components A Long-Term Commitment Needed

33 Advancing Biological Grid Grid Plumbing & Security Infrastructure SchedulingAccountingAuthorisation MonitoringDiagnosisLogging Scientific Application Data & Compute Resources Distributed Biological Users Data Access Data Integration Structured Data Biomedical (Grid) Application Component Library

34 Summary e-Science Data as well as Compute Challenges Needed to be put together Need ubiquitous supported consistent platforms Grid A (potentially) invaluable platform Only show in town Data Integration Hard Develop & Use Standard kit of parts Started to build the kit Opportunities No one-size fits all, but re-usable subsystems Invest in wider range of Problem driven pioneering Strategic choices needed


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